Quran 9:5 Kill the disbelievers wherever you find them ?!

9:5 Kill the disbelievers wherever you find them.

This ayah has been misquoted . First, we shall provide the verse in its context: 

فَإِذَا انسَلَخَ الْأَشْهُرُ‌ الْحُرُ‌مُ فَاقْتُلُوا الْمُشْرِ‌كِينَ حَيْثُ وَجَدتُّمُوهُمْ وَخُذُوهُمْ وَاحْصُرُ‌وهُمْ وَاقْعُدُوا لَهُمْ كُلَّ مَرْ‌صَدٍ ۚ فَإِن تَابُوا وَأَقَامُوا الصَّلَاةَ وَآتَوُا الزَّكَاةَ فَخَلُّوا سَبِيلَهُمْ ۚ إِنَّ اللَّـهَ غَفُورٌ‌ رَّ‌حِيمٌ ﴿٥﴾ وَإِنْ أَحَدٌ مِّنَ الْمُشْرِ‌كِينَ اسْتَجَارَ‌كَ فَأَجِرْ‌هُ حَتَّىٰ يَسْمَعَ كَلَامَ اللَّـهِ ثُمَّ أَبْلِغْهُ مَأْمَنَهُ ۚ ذَٰلِكَ بِأَنَّهُمْ قَوْمٌ لَّا يَعْلَمُونَ ﴿٦﴾

9:5-6 But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for Allah is Oft-forgiving, Most Merciful. If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah. and then escort him to where he can be secure. That is because they are men without knowledge.

Having presented the verse in context, we can analyze it properly. Dr. Maher Hathout gives an explanation on the historical context of the verse:

This verse was revealed towards the end of the revelation period and relates to a limited context. Hostilities were frozen for a three-month period during which the Arabs pledged not to wage war. Prophet Muhammad was inspired to use this period to encourage the combatants to join the Muslim ranks or, if they chose, to leave the area that was under Muslims rule; however, if they were to resume hostilities, then the Muslims would fight back until victorious. One is inspired to note that even in this context of war, the verse concludes by emphasizing the divine attributes of mercy and forgiveness. To minimize hostilities, the Qur'an ordered Muslims to grant asylum to anyone, even an enemy, who sought refuge. Asylum would be granted according to the customs of chivalry; the person would be told the message of the Qur'an but not coerced into accepting that message. Thereafter, he or she would be escorted to safety regardless of his or her religion. (9:6). (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, pp.52-53, emphasis added)

Therefore, this verse once again refers to those pagans who would continue to fight after the period of peace. It clearly commands the Muslims to protect those who seek peace and are non-combatants. It is a specific verse with a specific ruling and can in no way be applied to general situations. The command of the verse was only to be applied in the event of a battle. As Abdullah Yusuf Ali writes:

The emphasis is on the first clause: it is only when the four months of grace are past, and the other party show no sign of desisting from their treacherous design by right conduct, that the state of war supervenes - between Faith and Unfaith. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary, emphasis added)

If the pagans would not cease their hostilities towards the Muslims, then they were to be fought, especially since they were living in the land of an Islamic state. Dr. Zakir Naik writes concerning this verse:

This verse is quoted during a battle. ...We know that America was once at war with Vietnam. Suppose the President of America or the General of the American Army told the American soldiers during the war: "Wherever you find the Vietnamese, kill them". Today if I say that the American President said, "Wherever you find Vietnamese, kill them" without giving the context, I will make him sound like a butcher. But if I quote him in context, that he said it during a war, it will sound very logical, as he was trying to boost the morale of the American soldiers during the war. ...Similarly in Surah Taubah chapter 9 verse 5 the Qur'an says, "Kill the Mushriqs (pagans) where ever you find them", during a battle to boost the morale of the Muslim soldiers. What the Qur'an is telling Muslim soldiers is, don't be afraid during battle; wherever you find the enemies kill them. Surah Taubah chapter 9 verse 6 gives the answer to the allegation that Islam promotes violence, brutality and bloodshed. It says: "If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge." [Al-Qur'an 9:6]
The Qur'an not only says that a Mushriq seeking asylum during the battle should be granted refuge, but also that he should be escorted to a secure place. In the present international scenario, even a kind, peace-loving army General, during a battle, may let the enemy soldiers go free, if they want peace. But which army General will ever tell his soldiers, that if the enemy soldiers want peace during a battle, don't just let them go free, but also escort them to a place of security? This is exactly what Allah (swt) says in the Glorious Qur'an to promote peace in the world. (SOURCE, emphasis added)

Dr. Naik makes some very interesting observations about the verse. Indeed, it is truly amazing how Islam-haters will ignore God's infinite mercy in their attempt to malign Islam. God has always given human beings a way out of any suffering, and has only ordained fighting as a last resort. Muslim scholars have written much commentary on these Qur'anic verses explaining the historical context in such great detail so that there may be no misconceptions. We have quoted extensively from various commentators on these verses and there is no need to repeat the same material again. We will provide one more commentary before moving on. Professor Shahul Hameed writes on verse 9:5:

This is a verse taken from Surah At-Tawba. This chapter of the Qur’an was revealed in the context when the newly organized Muslim society in Madinah was engaged in defending themselves against the pagan aggressors. The major question dealt with here is, as to how the Muslims should treat those who break an existing treaty at will. The first clause in the verse refers to the time-honored Arab custom of a period of warning and waiting given to the offenders, after a clear violation. That is, they will be given four months’ time to repair the damage done or make peace. But if nothing happens after the expiry of these forbidden months, what should be done? This is what the present verse says. According to this verse, fighting must be resumed until one of the two things happens: Either the enemy should be vanquished by relentless fighting. That is what is meant by {then fight and slay the pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem [of war]}; or they should repent, establish prayers and pay zakah, etc. This is one of those verses of the Qur’an which are likely to be misunderstood, if quoted out of context. We must understand that this fighting was against a people who forced the Prophet and his companions to leave not only their own homes but all their property and even their hometown of Makkah to Madinah. Once the Muslims were organized into a community in those lawless times, the rules to be followed by the Muslims were clearly laid down, even in the matter of war. Since Islam is a comprehensive system, no human activity could be ignored. And given the nature of mankind, we cannot imagine a situation where fighting is completely ruled out either. As can be seen, the above injunctions on fighting is not on an individual level, but only in the case of a society that strives to flourish and thrive as a nation. But even here the norms are clear: fighting is only in self defence or for the establishment of justice; and always fighting is the last option. And no one is allowed to transgress the limits set by God. (SOURCE, emphasis added)

Ibn al-`Arabi, in his commentary on the Qur’an, writes:

“It is clear from this that the meaning of this verse is to kill the pagans who are waging war against you.” (Ahkam al-Qur’an: 2/456, emphasis added)

Shaykh Sami al-Majid also makes some very interesting points in his discussion on this verse:

If we look at the verses in Sûrah al-Tawbah immediately before and after the one under discussion, the context of the verse becomes clear. A few verses before the one we are discussing, Allah says: “There is a declaration of immunity from Allah and His Messenger to those of the pagans with whom you have contracted mutual alliances. Go then, for four months, to and fro throughout the land. But know that you cannot frustrate Allah that Allah will cover with shame those who reject Him.” [Sûrah al-Tawbah: 1-2]
In these verses we see that the pagans were granted a four month amnesty with an indication that when the four months were over, fighting would resume. However, a following verse exempts some of them from the resumption of hostilities. It reads:
“Except for those pagans with whom you have entered into a covenant and who then do not break their covenant at all nor aided anyone against you. So fulfill your engagements with them until the end of their term, for Allah loves the righteous.” [Sûrah al-Tawbah: 4]
So when Allah says: “But when the forbidden months are past, then fight the pagans wherever you find them, and seize them and beleaguer them and lie in wait for them in every stratagem (of war)” we must know that it is not general, since the verse above has qualified it to refer to the pagan Arabs who were actually at war with the Prophet (peace be upon him) and those who broke their covenants of peace. This is further emphasized a few verses later where Allah says:
“Will you not fight people who broke their covenants and plotted to expel the Messenger and attacked you first?” [Sûrah al-Tawbah: 13] (SOURCE)

Therefore, the context of the verse within the Surah makes it clear that this refers to those who are persistent in their hostilities and attacks against Muslims, and it is applied in battle only. We recommend that one reads Shaykh Sami Al-Majid's full article entitled There is no Compulsion in Religion.